//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
}else if (types[i] == "accnos") {
m->setAccnosFile("");
}else if (types[i] == "taxonomy") {
- m->setTaxonomyFile("");
+ m->setTaxonomyFile("");
+ }else if (types[i] == "flow") {
+ m->setFlowFile("");
+ }else if (types[i] == "processors") {
+ m->setProcessors("1");
}else if (types[i] == "all") {
m->clearCurrentFiles();
}else {
}
}
- m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
- m->printCurrentFiles();
+ if (m->hasCurrentFiles()) {
+ m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
+ m->printCurrentFiles();
+ }
return 0;
}